AvrDude

Can program AVR chips via serial from file.

AVRDUDE can be used effectively via the command line to read or write all chip memory types (eeprom, flash, fuse bits, lock bits, signature bytes) or via an interactive (terminal) mode. Using AVRDUDE from the command line works well for programming the entire memory of the chip from the contents of a file, while interactive mode is useful for exploring memory contents, modifying individual bytes of eeprom, programming fuse/lock bits, etc.

AVRDUDE tutorial

Some info on uploading on the Eclipse page

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